Description

BA 0346 is a phosphoramidite of a small, fluorescent nucleoside that is an isosteric mimic of thymidine.1,2 This probe has been shown to pair with adenine to form a stable duplex.
DNA probes constructed to contain BA 0346 at a selected sequence position show a significant emission enhancement when hybridization results in an opposing abasic residue as compared to an opposing adenine residue.1 This property makes BA 0346 useful for the preparation of probes that are designed to detect sequence-specific depurination and depyrimidination.

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Description

Tor and co-workers have reported on the preparation and photophysical characteristics of a number of small, fluorescent isosteric nucleosides that are capable of normal Watson-Crick base paring in unaltered duplexes.1-6 These probes are useful tools for studying nucleic acid sequence, structure, dynamics and recognition. BA 0347 is the phosphoramidite of one such nucleoside.1,2 This probe is a minimally disruptive fluorescent dC analog that can be used in vitro for analysis of oxidative damage caused by reactive oxygen species.6 When incorporated into an oligonucleotide and hybridized, BA 0347 can photophysically distinguish between G, 8-oxoG, or T on the complementary strand. When paired with 8-oxoG, which is the major mutagenic product of oxidative damage, significant emission quenching is observed. When paired with T, the transversion mutation resulting from failure to repair the oxidation, enhanced emission is observed from BA 0347.

Description

Description

The use of oxime formation in ligation reactions of oligonucleotides has been widely established in the literature for over a decade.1 As examples, 5’-aminooxy-modifiers have been used in oxime ligation for peptide-oligonucleotide conjugates,2 attachment of nucleosides to solid supports,3 and head to tail cyclization of oligonucleotides.4
The concurrent use of BA 0350 at the 5’-terminus and an indole aldehyde modification elsewhere in an oligonucleotide should permit on-support head to tail cyclization upon cleavage of the N-DMT protecting group. See Formylindole-dTCEP (BA 0301) for an example of an appropriate indole aldehyde.

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Description

We have discovered that DNA synthesis is markedly enhanced by including ether functionality in the alkyl chain of the disulfide. Both superior oligo yield and greater maximum synthesis length are thereby
achieved. We now offer Thiol-modifier-oxa-6-S-S CPG (BA 0351) as an alternative for 3'-thiol modification in oligonucleotides.

Notes

Description

Ogasawara and co-workers have reported the use of 8-substituted dG derivatives that provide reversible duplex regulation via a light induced trans-cis isomerization.1,2 The trans isomer of 8-styryl-2’-deoxyguanosine (8STG) is one such photochromic nucleoside (PCN). When a 12-bp duplex containing 8STG is irradiated for 5 minutes at 370 nm, the double bond isomerizes to the cis geometry with 86% conversion. Subsequent irradiation for 2 minutes at 254 nm returns the double bond to the trans geometry with 94% conversion. Both trans and cis isomers are thermally stable but readily interconvert at room temperature upon irradiation with light of the appropriate wavelength. The Tm value of the duplex containing a trans -PCN is 7.9oC higher than the Tm value of the same duplex containing a cis-PCN. When three 8STG insertions are inserted into a 20-bp duplex, the trans -PCNs permit duplex formation whereas the cis-PCNs cause denaturation of the duplex. This phenomenon is evidenced by changes in the circular dichroism spectra before and after irradiation of the duplex containing trans -PCNs at 370 nm. Conversely, when the single strands containg cis-PCNs are irradiated at 254 nm hybridization occurs as the trans isomer is formed.

Substitution of other aromatic moieties for the phenyl ring provides PCNs that operate at different wavelengths. For example with 8-(2-napthalen-2-yl)vinly-2’-deoxyguanosine (8NVG) the trans to cisconversion occurs with 410 nm irradiation and reverts at 290 nm and with 8-(2-fluoren-2-yl)vinyl-2’-deoxyguanosine (8FVG) ) the trans to cisconversion occurs with 420 nm irradiation and reverts at 310 nm. 8STG, 8NVG, and 8FVG all have the common synthetic precursor 8-vinyl-dG. Thus we now also offer PR 3335. as a versatile synthetic intermediate for the preparation of these and other PCNs.

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Description

Oligonucleotides with 5-ethynyl residues may be used in transition metal-catalyzed coupling reactions. Two ethynyl-bearing oligonucleotides can be homo-coupled via a diyne linkage using copper catalysis. Further, the ethynyl groups may be used in copper-catalyzed couplings with arylacetylenes bearing anthraquinone, biotin, or fluorescein appendages.1 Palladium catalyzed cross-coupling of ethynyl-dU-bearing oligonucleotidies with 2-iodoanthraquinone provides anthraquinone-bearing nucleic acids useful in electrochemical applications of DNA.2

For more detail on the use of this product, download a Product Information Sheet here.

Description

The (fluorenylmethyloxy)carbonyl (Fmoc) group has been shown to be useful as an amine protecting group on oligonucleotide amino-modifiers.1 It can be removed by standard cleave-deprotect protocols such as ammonium hydroxide. Alternatively, the Fmoc group can be selectively removed before cleavage of the oligonucleotide from the solid support,2 thereby simplifying labeling of the resulting amino group by acylation. After the acylation is complete and excess reagents are washed away, the labeled oligonucleotide is cleaved from the support and further deprotected with ammonium hydroxide.

See the Related Products below for additional product offerings that contain the Fmoc protecting group.

For more information on this product and its use, download a Product Information Sheet here.

Description

Electrochemical detection is a less expensive alternative to common optical methods in DNA biosensors and chips. Hocek and coworkers1 have shown that when aminophenyl (BA 0342) and nitrophenyl (BA 0355) substituted 2’-deoxyribonucleosides are incorporated into oligonucleotides, they exhibit excellent electrochemical label properties. Both types of markers in the same oligonucleotide can be easily detected and differentiated since the aminophenyl tag is irreversibly oxidized, and the nitophenyl tag is irreversibly reduced.

For more information on this product and its use, download a Product Information Sheet here.

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Description

Pyrrolo-C (PC) is a fluorescent analog of cytidine.1 It is highly fluorescent, the 2'-deoxy version exhibiting an emission maximum at 473 nm when incorporated into a 19-mer oligodeoxyribonucleotide, where it base-pairs normally with dG. Pyrrolo-C has proven to be useful for monitoring RNA secondary structure formation, where its fluorescence is reversibly quenched upon base-pairing.2 PC has been used to follow the kinetics of formation and dissociation of an RNA/DNA complex and has been used to monitor the thermal denaturation of the central segment of an RNA duplex.2 Most recently, PC has been incorporated into native and minimal hammerhead ribozymes at cleavage site position C17, where it was found to be capable of efficient photocrosslinking to G12, resulting in catalytically active RNA that was useful in structural studies.3

We also offer the 2’-OTBS phosphoramidite of pyrrolo-C (BA 0245) as well as the 2'-deoxyribo version, pyrrolo-dC CEP (BA 0170). These materials are also available from Glen Research (Pyrrolo-C CEP as the 2'-O-TOM version), our development partner for these products. Glen Research also offers the triphosphates of pyrrolo-C and -dC. We offer the two nucleosides (PYA 11090 and PYA 11092) as well as the simple fluorescent pyrrolocytosine heterocycle (i.e., pyrrolo-C aglycone (HC 9060). Thompson and co-workers have studied the photophysical properties of these fluorescent pyrrolopyrimidines.4

For more detail on the use of this product, download a Product Information Sheet here.

Notes

Description

In the search for effective in vivo carriers for therapeutic applications of siRNAs, Nishina, Unno and coworkers utilized alpha-tocopherol (vitamin E) as a carrier molecule.1 They hypothesized that a molecule that had its own transport pathway, was essential for target tissue cells, yet was not synthesized within the cells would be an ideal in vivo carrier conjugate. Their results indicate that alpha -tocopherol is a safe and effective carrier for delivery of siRNA into the liver. Following their lead, we have modified alpha -tocopherol with the mixed polarity TEG linker, and produced the corresponding phosphoramidite (BA 0357) which is useful for modification of oligonucleotides either internally or at the 5’-terminus.

Description

This compound is sold under license from baseclick GmbH, and the purchase of these products for use in applications relating to copper catalyzed azide-alkyne cycloaddition chemistry (“Click Chemistry”) includes a limited, nontransferable license to intellectual property owned by TSRI to use this product solely for internal non-commercial research activities and specifically excludes clinical, therapeutic, or diagnostic use in humans or animals. Information regarding a license for commercial use in Click Chemistry may be obtained directly from The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, or by contacting 858-784-8140 or click@scripps.edu.

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Description

This compound is sold under license from baseclick GmbH, and the purchase of these products for use in applications relating to copper catalyzed azide-alkyne cycloaddition chemistry (“Click Chemistry”) includes a limited, nontransferable license to intellectual property owned by TSRI to use this product solely for internal non-commercial research activities and specifically excludes clinical, therapeutic, or diagnostic use in humans or animals. Information regarding a license for commercial use in Click Chemistry may be obtained directly from The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, or by contacting 858-784-8140 or click@scripps.edu.

Alternate Name(s):

Description

This compound is sold under license from baseclick GmbH, and the purchase of these products for use in applications relating to copper catalyzed azide-alkyne cycloaddition chemistry (“Click Chemistry”) includes a limited, nontransferable license to intellectual property owned by TSRI to use this product solely for internal non-commercial research activities and specifically excludes clinical, therapeutic, or diagnostic use in humans or animals. Information regarding a license for commercial use in Click Chemistry may be obtained directly from The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, or by contacting 858-784-8140 or click@scripps.edu.

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Description

2’-Deoxycytidine methylation is an important and well studied modification of DNA. The cytosine methylation alters DNA structure without impacting base pairing. This modification affects binding of transcription factors and subsequent gene express and is, therefore, an important epigenetic marker. For the human p53 gene, the predominant mutation is a C to T transition, and Matsuda and co-workers have reported findings that indicate this transition can be caused by the formation of 5-formyl-2’-deoxycytidine.1 Based on their findings, we have introduced BA 0367 into our product line and a useful tool for further studies.

Description

This compound is sold under license from baseclick GmbH, and the purchase of these products for use in applications relating to copper catalyzed azide-alkyne cycloaddition chemistry (“Click Chemistry”) includes a limited, nontransferable license to intellectual property owned by TSRI to use this product solely for internal non-commercial research activities and specifically excludes clinical, therapeutic, or diagnostic use in humans or animals. Information regarding a license for commercial use in Click Chemistry may be obtained directly from The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, or by contacting 858-784-8140 or click@scripps.edu.

Description

2’-Deocycytodine methylation is an important and well studied modification of DNA. The cytosine methylation alters DNA structure without impacting base pairing. This modification affects binding of transcription factors and subsequent gene express and is, therefore, an important epigenetic marker.

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Description

The click cycloaddition reaction is a remarkably efficient and reliable process for bioconjugation even in the presence of the diverse array of functional groups found in DNA and the variety of scientifically intriguing ligation partners. Our 5’-Click-easyTM BCN CEP (BA 0372)1 can be used to prepare oligonucleotides for subsequent clean and efficient copper-free click cycloaddition. In our hands, the bicyclo[6.1.0]nonyne (BCN)2 is a superior scaffold for the strain-promoted alkyne-azide cycloaddition.3

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Description

The click cycloaddition reaction is a remarkably efficient and reliable process for bioconjugation even in the presence of the diverse array of functional groups found in DNA and the variety of scientifically intriguing ligation partners. Our 5’-Click-easyTM BCN CEP (BA 0373)1 can be used to prepare oligonucleotides for subsequent clean and efficient copper-free click cycloaddition. In our hands, the bicyclo[6.1.0]nonyne (BCN)2 is a superior scaffold for the strain-promoted alkyne-azide cycloaddition.3

Alternate Name(s):

Description

The use of oxime formation in ligation reactions of oligonucleotides has been widely established in the literature for over a decade.1 As examples, 5’-aminooxy-modifiers have been used in oxime ligation for peptide-oligonucleotide conjugates,2 attachment of nucleosides to solid supports,3 and head to tail cyclization of oligonucleotides.4